The move has seen Putin's approval rating drop by 15% and "unlike protests against corruption organised by Navalny, which have rallied mostly young people, the pension protests have brought older Russians, often seen as Mr Putin's base, into the streets", says the New York Times.
In Khabarovsk, incumbent Governor Vyacheslav Shport of United Russia garnered 35.6 percent of the vote and was narrowly edged out by Sergei Furgal, a federal lawmaker from the nationalist Liberal Democratic Party (LDPR), according to official results.
More than 2,500 people gathered in Moscow's Pushkin Square shouting "Putin is a thief!" and "No increase in the pension age!"
Putin thanked Russians for voting, saying the election results underscored their trust in the authorities.
In Moscow, Sobyanin is expected to be returned to city hall with around 70 percent of the vote, on turnout of 30 to 40 percent. Navalny has likened Putin to an autocratic tsar who has clung to power for too long. Its strong showing came in part thanks to strict restrictions that prevented opposition candidates getting on the ballot, as well as domination of state media.
Another protester, Katya Shomnikova, 23, said: "They (the authorities) stole my future life, we will have to correct what's been done".
The ruling party suffered several major upsets.
Alexei Makarkin, an analyst at the Center for Political Technologies, said Russians are exhausted of "the long, punishing crisis whose end is nowhere in sight" and have stopped voting for the ruling party by default.
"They're spending money on the army in Syria, in Ukraine, for the president's friends, but nothing for pensioners", Olga Chenushka, a 44-year-old finance manager told AFP.
The rallies were called by the jailed opposition leader Alexei Navalny, who has capitalised on widespread anger against the reforms.
Almost half of those detained were rounded up in St. Petersburg, according to the OVD-Info.
As in previous rallies, numerous protesters were young, including minors, and pictures of the police manhandling teens went viral on social media.
Navalny's group said its St. Petersburg coordinator and another of its activists were detained in St. Petersburg as well.
It is known that two criminal cases over the use of violence against police officers are initiated.
Observers noted fewer people turned up to protest against the reform than in May after Putin softened the pension reform.
After being amended by Putin, the reforms envisage raising the retirement age for men to 65 from 60 and to 60 from 55 for women.
Supporters say Sobyanin has transformed the city with billion-dollar renovation projects that include a showpiece central park and new pedestrian areas along with a string of new metro stations.